Flow cytometry analysisAI-assisted gating
The problem
Manual gating is a bottleneck
Repetitive, subjective, and slow. Your time should go to biology, not drawing rectangles.
hours / week
Wasted on repetitive gating
Same panels, same gates, hundreds of files. Over and over.
inter-analyst variability reported
A documented reproducibility challenge
Published studies¹ show significant gating disagreement even among experienced cytometrists. Two analysts, same data, different results — and reviewers notice.
cloud-native AI gating tools available
The market hasn't caught up
Most flow cytometry analysis software was designed before cloud computing and machine learning were practical. Cytomaton starts from a different foundation.
¹ Aghaeepour et al., “Critical assessment of automated flow cytometry data analysis techniques,” Nature Methods 10, 228–238 (2013)
Features
Spectral-native. Cloud-first. AI-powered.
Not a desktop tool with cloud bolted on. Built from scratch for modern flow cytometry.
AI gating that learns from you
After 3+ manual gates on a panel, the AI suggests boundaries for new samples. Every gate you draw makes it smarter. Your conventions, learned automatically.
Universal FCS import
Drop files from any cytometer — BD, Cytek, Beckman, Sony. Automatic parameter mapping. No vendor-specific plugins needed.
Cloud collaboration
Share gating analyses with your PI or collaborators in one click — no FCS file attachments, no version confusion. Review gating strategies together, live, from any browser.
Spectral unmixing
Native support for 30–50 parameter spectral panels from day one. AI flags potential unmixing artifacts before you start.
Batch processing
Save your gating strategy as a template and apply it to up to 100 files per batch job. Per-sample statistics aggregated to CSV — including MFI for every parameter.
Publication-ready export
Direct GraphPad Prism export, PowerPoint slides, PNG (300 DPI), SVG, and PDF — with proper axis labels and statistics tables. MIFlowCyt metadata for NIH compliance. Clipboard-to-Excel for quick analysis.
More capabilities
FlowSOM clustering
Automated cell population identification with phenotype labeling. Integrates with UMAP/tSNE embeddings and expression heatmaps.
UMAP, tSNE & PCA
Explore high-dimensional data with native dimensionality reduction. Back-gate from embeddings directly to scatter plots.
AI flow cytometry assistant
A domain-expert AI chat panel that knows your loaded files, current gates, and analysis context. Choose from multiple AI models or bring your own API key.
FlowJo workspace import
Bring your FlowJo gating strategies to Cytomaton. Import .wsp files directly — no rebuilding from scratch.
Automated data QC
Time-gate anomaly detection, doublet rate assessment, and event count checks — automatically flagged before you start gating.
GraphPad Prism export
Export gating statistics directly to Prism (.pzfx) — Column, Grouped, or XY layouts. Plus PowerPoint slides and MIFlowCyt metadata for NIH compliance.
How it works
Three steps to AI-assisted gating
Upload your FCS files
Drag and drop from any cytometer. Cytomaton auto-detects parameters, compensation matrices, and cytometer type.
Gate a few samples
Draw your gates the way you normally would. The AI watches, learns your lab's conventions, panel by panel.
Let AI take over
New samples get AI-suggested gates automatically. Review, adjust, or accept in one click — you're always in control.
Who it's for
Built for the bench, not the boardroom
Independent. Not owned by an instrument manufacturer or platform company. Built by researchers, for researchers.
Research scientists
Spend your time on biology, not gating. Cut 2–10 hours of weekly gating work to minutes with AI-assisted analysis.
Core facilities
Shared templates, centralized management, consistent gating across your entire facility. One account for your whole team.
High-throughput labs
Process hundreds of samples per run with batch gating and AI suggestions tuned to your specific panels and protocols.
Why Cytomaton
Your data. Your gates. Your choice.
Most flow cytometry analysis software is now owned by instrument manufacturers or large platform companies. That can mean product decisions driven by corporate strategy rather than researcher needs. Cytomaton is independently built — we don't sell instruments, so we optimize for every instrument brand equally. Product decisions are driven by what helps you do better science.
Ready to gate smarter?
Join the closed beta. We review every application — spots are limited.
Questions? Email us at hello@cytomaton.ai